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Qin S, Wei G, Lin Q, Tang D, Li C, Tan Z, Yao L, Huang L, Wei F, Liang Y. Analysis of the Spatholobus suberectus full-length transcriptome identified an R2R3-MYB transcription factor-encoding gene SsMYB158 that regulates flavonoid biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108929. [PMID: 39002304 DOI: 10.1016/j.plaphy.2024.108929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/14/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
Spatholobus suberectus Dunn (Leguminosae) has been used for medicinal purposes for a long period. Flavonoids are the major bioactive components of S. suberectus. However, there is still limited knowledge of the exact method via which transcription factors (TFs) regulate flavonoid biosynthesis. The full-length transcriptome of S. suberectus was analyzed using SMRT sequencing; 61,548 transcripts were identified, including 12,311 new gene loci, 53,336 novel transcripts, 44,636 simple sequence repeats, 36,414 complete coding sequences, 871 long non-coding RNAs and 6781 TFs. The SsMYB158 TF, which is associated with flavonoid biosynthesis, belongs to the R2R3-MYB class and is localized subcellularly to the nucleus. The overexpression of SsMYB158 in Nicotiana benthamiana and the transient overexpression of SsMYB158 in S. suberectus resulted in a substantial enhancement in both flavonoids and catechin levels. In addition, there was a remarkable upregulation in the expression of essential enzyme-coding genes associated with the flavonoid biosynthesis pathways. Our study revealed SsMYB158 as a critical regulator of flavonoid biosynthesis in S. suberectus and laying the foundation for its molecular breeding.
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Affiliation(s)
- Shuangshuang Qin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Guili Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Quan Lin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Danfeng Tang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Cui Li
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhien Tan
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lixiang Yao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lirong Huang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Ying Liang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
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D'Incà R, Mattioli R, Tomasella M, Tavazza R, Macone A, Incocciati A, Martignago D, Polticelli F, Fraudentali I, Cona A, Angelini R, Tavazza M, Nardini A, Tavladoraki P. A Solanum lycopersicum polyamine oxidase contributes to the control of plant growth, xylem differentiation, and drought stress tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:960-981. [PMID: 38761363 DOI: 10.1111/tpj.16809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/26/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024]
Abstract
Polyamines are involved in several plant physiological processes. In Arabidopsis thaliana, five FAD-dependent polyamine oxidases (AtPAO1 to AtPAO5) contribute to polyamine homeostasis. AtPAO5 catalyzes the back-conversion of thermospermine (T-Spm) to spermidine and plays a role in plant development, xylem differentiation, and abiotic stress tolerance. In the present study, to verify whether T-Spm metabolism can be exploited as a new route to improve stress tolerance in crops and to investigate the underlying mechanisms, tomato (Solanum lycopersicum) AtPAO5 homologs were identified (SlPAO2, SlPAO3, and SlPAO4) and CRISPR/Cas9-mediated loss-of-function slpao3 mutants were obtained. Morphological, molecular, and physiological analyses showed that slpao3 mutants display increased T-Spm levels and exhibit changes in growth parameters, number and size of xylem elements, and expression levels of auxin- and gibberellin-related genes compared to wild-type plants. The slpao3 mutants are also characterized by improved tolerance to drought stress, which can be attributed to a diminished xylem hydraulic conductivity that limits water loss, as well as to a reduced vulnerability to embolism. Altogether, this study evidences conservation, though with some significant variations, of the T-Spm-mediated regulatory mechanisms controlling plant growth and differentiation across different plant species and highlights the T-Spm role in improving stress tolerance while not constraining growth.
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Affiliation(s)
- Riccardo D'Incà
- Department of Science, University Roma Tre, 00146, Rome, Italy
| | | | - Martina Tomasella
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Raffaela Tavazza
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), BIOAG-BIOTEC C.R. Casaccia, Rome, Italy
| | - Alberto Macone
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome, Rome, Italy
| | - Alessio Incocciati
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome, Rome, Italy
| | | | - Fabio Polticelli
- Department of Science, University Roma Tre, 00146, Rome, Italy
- National Institute of Nuclear Physics, Roma Tre Section, 00146, Rome, Italy
| | | | - Alessandra Cona
- Department of Science, University Roma Tre, 00146, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi (INBB), Rome, Italy
| | - Riccardo Angelini
- Department of Science, University Roma Tre, 00146, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi (INBB), Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Mario Tavazza
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), BIOAG-BIOTEC C.R. Casaccia, Rome, Italy
| | - Andrea Nardini
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Paraskevi Tavladoraki
- Department of Science, University Roma Tre, 00146, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi (INBB), Rome, Italy
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Mishra LS, Cook SD, Kushwah S, Isaksson H, Straub IR, Abele M, Mishra S, Ludwig C, Libby E, Funk C. Overexpression of the plastidial pseudo-protease AtFtsHi3 enhances drought tolerance while sustaining plant growth. PHYSIOLOGIA PLANTARUM 2024; 176:e14370. [PMID: 38818570 DOI: 10.1111/ppl.14370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024]
Abstract
With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass and quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 (FtsHi3OE) enhances drought-tolerant phenotypes without compromising plant growth. AtFtsHi3 encodes a chloroplast envelope pseudo-protease; knock-down mutants (ftshi3-1) are found to be drought tolerant but exhibit stunted growth. Altered AtFtsHi3 expression therefore leads to drought tolerance, while only diminished expression of this gene leads to growth retardation. To understand the underlying mechanisms of the enhanced drought tolerance, we compared the proteomes of ftshi3-1 and pFtsHi3-FtsHi3OE (pFtsHi3-OE) to wild-type plants under well-watered and drought conditions. Drought-related processes like osmotic stress, water transport, and abscisic acid response were enriched in pFtsHi3-OE and ftshi3-1 mutants following their enhanced drought response compared to wild-type. The knock-down mutant ftshi3-1 showed an increased abundance of HSP90, HSP93, and TIC110 proteins, hinting at a potential downstream role of AtFtsHi3 in chloroplast pre-protein import. Mathematical modeling was performed to understand how variation in the transcript abundance of AtFtsHi3 can, on the one hand, lead to drought tolerance in both overexpression and knock-down lines, yet, on the other hand, affect plant growth so differently. The results led us to hypothesize that AtFtsHi3 may form complexes with at least two other protease subunits, either as homo- or heteromeric structures. Enriched amounts of AtFtsH7/9, AtFtsH11, AtFtsH12, and AtFtsHi4 in ftshi3-1 suggest a possible compensation mechanism for these proteases in the hexamer.
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Affiliation(s)
| | - Sam D Cook
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Hanna Isaksson
- Department of Mathematics and Mathematical Statistics, Integrated Science Lab (Icelab), Umeå University, Umeå, Sweden
- IceLab, Umeå University, Umeå, Sweden
| | - Isabella R Straub
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Sanatkumar Mishra
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Eric Libby
- Department of Mathematics and Mathematical Statistics, Integrated Science Lab (Icelab), Umeå University, Umeå, Sweden
- IceLab, Umeå University, Umeå, Sweden
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4
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Mei G, Chen A, Wang Y, Li S, Wu M, Hu Y, Liu X, Hou X. A simple and efficient in planta transformation method based on the active regeneration capacity of plants. PLANT COMMUNICATIONS 2024; 5:100822. [PMID: 38243598 PMCID: PMC11009361 DOI: 10.1016/j.xplc.2024.100822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 09/18/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024]
Abstract
Plant genetic transformation strategies serve as essential tools for the genetic engineering and advanced molecular breeding of plants. However, the complicated operational protocols and low efficiency of current transformation strategies restrict the genetic modification of most plant species. This paper describes the development of the regenerative activity-dependent in planta injection delivery (RAPID) method based on the active regeneration capacity of plants. In this method, Agrobacterium tumefaciens is delivered to plant meristems via injection to induce transfected nascent tissues. Stable transgenic plants can be obtained by subsequent vegetative propagation of the positive nascent tissues. The method was successfully used for transformation of plants with strong regeneration capacity, including different genotypes of sweet potato (Ipomoea batatas), potato (Solanum tuberosum), and bayhops (Ipomoea pes-caprae). Compared with traditional transformation methods, RAPID has a much higher transformation efficiency and shorter duration, and it does not require tissue culture procedures. The RAPID method therefore overcomes the limitations of traditional methods to enable rapid in planta transformation and can be potentially applied to a wide range of plant species that are capable of active regeneration.
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Affiliation(s)
- Guoguo Mei
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ao Chen
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaru Wang
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuquan Li
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minyi Wu
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yilong Hu
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Liu
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Bekalu ZE, Panting M, Bæksted Holme I, Brinch-Pedersen H. Opportunities and Challenges of In Vitro Tissue Culture Systems in the Era of Crop Genome Editing. Int J Mol Sci 2023; 24:11920. [PMID: 37569295 PMCID: PMC10419073 DOI: 10.3390/ijms241511920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Currently, the development of genome editing (GE) tools has provided a wide platform for targeted modification of plant genomes. However, the lack of versatile DNA delivery systems for a large variety of crop species has been the main bottleneck for improving crops with beneficial traits. Currently, the generation of plants with heritable mutations induced by GE tools mostly goes through tissue culture. Unfortunately, current tissue culture systems restrict successful results to only a limited number of plant species and genotypes. In order to release the full potential of the GE tools, procedures need to be species and genotype independent. This review provides an in-depth summary and insights into the various in vitro tissue culture systems used for GE in the economically important crops barley, wheat, rice, sorghum, soybean, maize, potatoes, cassava, and millet and uncovers new opportunities and challenges of already-established tissue culture platforms for GE in the crops.
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6
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Oliveira-Garcia E, Tamang TM, Park J, Dalby M, Martin-Urdiroz M, Rodriguez Herrero C, Vu AH, Park S, Talbot NJ, Valent B. Clathrin-mediated endocytosis facilitates the internalization of Magnaporthe oryzae effectors into rice cells. THE PLANT CELL 2023:koad094. [PMID: 36976907 DOI: 10.1093/plcell/koad094] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Fungi and oomycetes deliver effectors into living plant cells to suppress defenses and control plant processes needed for infection. Little is known about the mechanism by which these pathogens translocate effector proteins across the plasma membrane into the plant cytoplasm. The blast fungus Magnaporthe oryzae secretes cytoplasmic effectors into a specialized biotrophic interfacial complex (BIC) before translocation. Here we show that cytoplasmic effectors within BICs are packaged into punctate membranous effector compartments that are occasionally observed in the host cytoplasm. Live cell imaging with fluorescently labeled proteins in rice (Oryza sativa) showed that these effector puncta colocalize with the plant plasma membrane and with CLATHRIN LIGHT CHAIN 1, a component of clathrin-mediated endocytosis (CME). Inhibiting CME using virus-induced gene silencing and chemical treatments resulted in cytoplasmic effectors in swollen BICs lacking effector puncta. By contrast, fluorescent marker co-localization, gene silencing and chemical inhibitor studies failed to support a major role for clathrin-independent endocytosis in effector translocation. Effector localization patterns indicated that cytoplasmic effector translocation occurs underneath appressoria before invasive hyphal growth. Taken together, this study provides evidence that cytoplasmic effector translocation is mediated by clathrin-mediated endocytosis in BICs and suggests a role for M. oryzae effectors in co-opting plant endocytosis.
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Affiliation(s)
- Ely Oliveira-Garcia
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Tej Man Tamang
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS 66506, USA
| | - Jungeun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS 66506, USA
| | - Melinda Dalby
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | | | - Clara Rodriguez Herrero
- School of Biosciences, University of Exeter, Exeter, EX4 4QD, UK
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - An Hong Vu
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Sunghun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS 66506, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
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7
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Pakuła K, Sequeiros-Borja C, Biała-Leonhard W, Pawela A, Banasiak J, Bailly A, Radom M, Geisler M, Brezovsky J, Jasiński M. Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters. Cell Mol Life Sci 2023; 80:105. [PMID: 36952129 PMCID: PMC10036432 DOI: 10.1007/s00018-023-04751-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
Abstract
ABCG46 of the legume Medicago truncatula is an ABC-type transporter responsible for highly selective translocation of the phenylpropanoids, 4-coumarate, and liquiritigenin, over the plasma membrane. To investigate molecular determinants of the observed substrate selectivity, we applied a combination of phylogenetic and biochemical analyses, AlphaFold2 structure prediction, molecular dynamics simulations, and mutagenesis. We discovered an unusually narrow transient access path to the central cavity of MtABCG46 that constitutes an initial filter responsible for the selective translocation of phenylpropanoids through a lipid bilayer. Furthermore, we identified remote residue F562 as pivotal for maintaining the stability of this filter. The determination of individual amino acids that impact the selective transport of specialized metabolites may provide new opportunities associated with ABCGs being of interest, in many biological scenarios.
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Affiliation(s)
- Konrad Pakuła
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614, Poznan, Poland
| | - Carlos Sequeiros-Borja
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Wanda Biała-Leonhard
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Aleksandra Pawela
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Joanna Banasiak
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Aurélien Bailly
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Marcin Radom
- Department of Structural Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z.Noskowskiego12/14, 61-704, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Markus Geisler
- Department of Biology, University of Fribourg, Chem. du Musée 10, 1700, Fribourg, Switzerland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, 02-109, Warsaw, Poland.
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland.
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632, Poznan, Poland.
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8
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Toh WK, Teo YL, Tor XY, Loh PC, Wong HL. Development of constitutive and IPTG-inducible integron promoter-based expression systems for Escherichia coli and Agrobacterium tumefaciens. 3 Biotech 2023; 13:91. [PMID: 36825259 PMCID: PMC9941393 DOI: 10.1007/s13205-023-03507-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Broad host range (BHR) expression vector is a vital tool in molecular biology research and application. Currently, most of the plasmid vectors used in Agrobacterium spp. are binary vectors that are designed for plant transformation, and very few are designed for expressing transgenes in Agrobacterium spp. Class 1 integrons are common genetic elements that allow for the efficient capture and expression of antibiotic resistance genes, especially in Gram-negative bacteria. One of its compound promoters, PcS + P2, was used in this study and has been reported to be the strongest class 1 integron constitutive promoter; it is referred to as "integron promoter" (P int) henceforth. Herein, we created two versions of isopropyl-d-thiogalactopyranoside (IPTG)-inducible promoters by substituting and/or inserting lacO sequence(s) into P int. These inducible promoters, which possess different degrees of stringency and inducibility, were used to construct two broad host range expression vectors (pWK102 and pWK103) based on the versatile pGREEN system. This allows them to be stably maintained and replicated in both Escherichia coli and Agrobacterium tumefaciens. Functional validation of these vectors was performed by the expression of the reporter gene, superfolder green fluorescent protein (sfGFP), which was cloned downstream of these promoters. Due to the strong induction and tunable expression of a transgene located downstream to the inducible integron promoter, these vectors may be useful for heterologous gene expression in both E. coli and A. tumefaciens, thus facilitating recombinant protein production and genetic studies in Gram-negative bacteria. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03507-0.
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Affiliation(s)
- Wai Keat Toh
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900 Kampar, Perak Malaysia
| | - Yuh Leng Teo
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900 Kampar, Perak Malaysia
| | - Xin Yen Tor
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900 Kampar, Perak Malaysia
| | - Pek Chin Loh
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900 Kampar, Perak Malaysia
| | - Hann Ling Wong
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900 Kampar, Perak Malaysia
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9
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Reasons and riddance of Agrobacterium tumefaciens overgrowth in plant transformation. Transgenic Res 2023; 32:33-52. [PMID: 36806963 DOI: 10.1007/s11248-023-00338-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
Agrobacterium tumefaciens-mediated plant transformation has become routine work across the world to study gene function and the production of genetically modified plants. However, several issues hamper the transformation process in a profound way, both directly and indirectly. One of the major concerns is the overgrowth of Agrobacterium, which occasionally appears after the co-cultivation phase of the explant. This phenomenon is reported in several species and seems to spoil the whole transformation process. There are multiple approaches being employed to counter this unwanted growth of bacteria in a few plant species. In reality, once the overgrowth appears, it becomes nearly impossible to cure it. Hence, for the prevention of this phenomenon, numerous factors are regulated. These factors are: explant nature, A. tumefaciens strain, T-DNA vector, co-cultivation (time and condition), acetosyringone, washing medium, antibiotics (type, concentration, combination, incubation period), etc. In this article, we discuss these factors based on available reports. It can be of immense help in formulating viable strategies to control A. tumefaciens overgrowth.
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10
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Mabuza LM, Mchunu NP, Crampton BG, Swanevelder DZH. Accelerated Breeding for Helianthus annuus (Sunflower) through Doubled Haploidy: An Insight on Past and Future Prospects in the Era of Genome Editing. PLANTS (BASEL, SWITZERLAND) 2023; 12:485. [PMID: 36771570 PMCID: PMC9921946 DOI: 10.3390/plants12030485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
The aim of any breeding process is to fully express the targeted, superior/desirable parent characteristic in the progeny. Hybrids are often used in this dynamic, and complex process for which homozygous parents-which may require up to eight generations of back crossing and selection-are required. Doubled haploid (DH) technologies can facilitate the production of true breeding lines faster and in a more efficient manner than the traditional back crossing and selection strategies. Sunflower is the third most important oilseed crop in the world and has no available double haploid induction procedure/technique that can be efficiently used in breeding programs. A reproducible and efficient doubled haploid induction method would be a valuable tool in accelerating the breeding of new elite sunflower varieties. Although several attempts have been made, the establishment of a sunflower doubled haploid induction protocol has remained a challenge owing recalcitrance to in vitro culture regeneration. Approaches for haploid development in other crops are often cultivar specific, difficult to reproduce, and rely on available tissue culture protocols-which on their own are also cultivar and/or species specific. As an out-crossing crop, the lack of a double haploid system limits sunflower breeding and associated improvement processes, thereby delaying new hybrid and trait developments. Significant molecular advances targeting genes, such as the centromeric histone 3 (CenH3) and Matrilineal (MTL) gene with CRISPR/Cas9, and the successful use of viral vectors for the delivery of CRISPR/Cas9 components into plant cells eliminating the in vitro culture bottleneck, have the potential to improve double haploid technology in sunflower. In this review, the different strategies, their challenges, and opportunities for achieving doubled haploids in sunflower are explored.
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Affiliation(s)
- Londiwe M. Mabuza
- Biotechnology Platform, Agricultural Research Council, Onderstepoort Campus, Onderstepoort, Pretoria 0110, South Africa
- Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Nokuthula P. Mchunu
- Biotechnology Platform, Agricultural Research Council, Onderstepoort Campus, Onderstepoort, Pretoria 0110, South Africa
- Strategy, Planning and Partnerships, National Research Foundation, Pretoria 0184, South Africa
| | - Bridget G. Crampton
- Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Dirk Z. H. Swanevelder
- Biotechnology Platform, Agricultural Research Council, Onderstepoort Campus, Onderstepoort, Pretoria 0110, South Africa
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11
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Garg V, Reins J, Hackel A, Kühn C. Elucidation of the interactome of the sucrose transporter StSUT4: sucrose transport is connected to ethylene and calcium signalling. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7401-7416. [PMID: 36124639 PMCID: PMC9730799 DOI: 10.1093/jxb/erac378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Sucrose transporters of the SUT4 clade show dual targeting to both the plasma membrane as well as to the vacuole. Previous investigations revealed a role for the potato sucrose transporter StSUT4 in flowering, tuberization, shade avoidance response, and ethylene production. Down-regulation of StSUT4 expression leads to early flowering, tuberization under long days, far-red light insensitivity, and reduced diurnal ethylene production. Sucrose export from leaves was increased and a phase-shift of soluble sugar accumulation in source leaves was observed, arguing for StSUT4 to be involved in the entrainment of the circadian clock. Here, we show that StSUT4, whose transcripts are highly unstable and tightly controlled at the post-transcriptional level, connects components of the ethylene and calcium signalling pathway. Elucidation of the StSUT4 interactome using the split ubiquitin system helped to prove direct physical interaction between the sucrose transporter and the ethylene receptor ETR2, as well as with the calcium binding potato calmodulin-1 (PCM1) protein, and a calcium-load activated calcium channel. The impact of calcium ions on transport activity and dual targeting of the transporter was investigated in detail. For this purpose, a reliable esculin-based transport assay was established for SUT4-like transporters. Site-directed mutagenesis helped to identify a diacidic motif within the seventh transmembrane spanning domain that is essential for sucrose transport activity and targeting, but not required for calcium-dependent inhibition. A link between sucrose, calcium and ethylene signalling has been previously postulated with respect to pollen tube growth, shade avoidance response, or entrainment of the circadian clock. Here, we provide experimental evidence for the direct interconnection of these signalling pathways at the molecular level by direct physical interaction of the main players.
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Affiliation(s)
- Varsha Garg
- Humboldt-Universität zu Berlin, Institute of Biology, Department of Plant Physiology, Philippstr. 13 Building 12, 10115 Berlin, Germany
| | - Jana Reins
- Humboldt-Universität zu Berlin, Institute of Biology, Department of Plant Physiology, Philippstr. 13 Building 12, 10115 Berlin, Germany
| | - Aleksandra Hackel
- Humboldt-Universität zu Berlin, Institute of Biology, Department of Plant Physiology, Philippstr. 13 Building 12, 10115 Berlin, Germany
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12
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Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes. PLoS Genet 2022; 18:e1010345. [PMID: 36084135 PMCID: PMC9491579 DOI: 10.1371/journal.pgen.1010345] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/21/2022] [Accepted: 07/16/2022] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have revealed that the striking natural variation for DNA CHH-methylation (mCHH; H is A, T, or C) of transposons has oligogenic architecture involving major alleles at a handful of known methylation regulators. Here we use a conditional GWAS approach to show that CHG-methylation (mCHG) has a similar genetic architecture—once mCHH is statistically controlled for. We identify five key trans-regulators that appear to modulate mCHG levels, and show that they interact with a previously identified modifier of mCHH in regulating natural transposon mobilization. DNA methylation is an epigenetic mark common across eukaryotes. It is associated with transcriptional silencing, in particular of transposable elements. Multiple elements, including epigenetic inheritance, shape DNA methylation patterns, and the complexity makes it challenging to dissect the regulation. Our work on the 1001 Arabidopsis Epigenomes project led to the unexpected discovery that much of the natural variation for CHH methylation (mCHH; H is A, T, or C) on transposable elements could be attributed to allelic variation in three genes known to be involved in epigenetic regulation. However, our analysis of methylation in other sequence contexts (mCHG and mCG) revealed no genetic regulator. Here we show that if mCHG variation is analyzed while taking mCHH into account, mCHG is also strongly influenced by allelic variation in a small number of genes with known or highly plausible direct roles in epigenetic regulation. The presence of common allelic variation of large effect is suggestive of some form of local adaptation. The nature of this adaptation remains obscure, but we present further evidence that allelic variation regulating DNA methylation influences transposon mobilization.
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13
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Spiegel H, Nölke G, Thangaraj H, Schillberg S. The concept of an agroinfiltration kit for recombinant protein production for educational and commercial use—A journey through a forest of regulatory and legal implications. Front Bioeng Biotechnol 2022; 10:926239. [PMID: 36131725 PMCID: PMC9483176 DOI: 10.3389/fbioe.2022.926239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Recombinant expression using Agrobacterium-mediated transient transformation (ATT) of plants has developed into a robust and versatile method to rapidly produce proteins. The capability of plants to efficiently synthesize even homo- and hetero-multimeric complex folded proteins featuring disulfide bonds and other post-translational modifications such as N-linked glycosylation makes them superior to most of the established microbial, especially prokaryotic expression hosts. Compared to production in mammalian cell cultures, ATT requires lower skills, simple technical equipment and cheaper media components. Taken together these features make the method optimally suited for R&D applications involving the development and engineering of recombinant proteins for various purposes ranging from vaccine candidates, therapeutic proteins, towards enzymes for different pharmaceutical and technical applications. Despite these advantages the technology is currently not being used outside the community of plant research. The design and realization of a kit containing all the information, instructions and ideally also the material required to perform recombinant protein production using ATT in an educational or commercial context was one of the objectives of the EU-funded Horizon 2020 project Pharma-Factory. While it is pretty straightforward to assemble a comprehensive instruction manual describing the procedure, the clarification of regulatory and legal aspects associated with the provision, dissemination and use of the different materials and organisms required to perform ATT is a complex matter. In this article, we describe the initial concept of an ATT kit for educational as well as research and development (R&D) purposes and the specific regulatory and legal implications associated with the various kit components. We cover aspects including intellectual property rights, freedom-to-operate (FTO), safety regulations for distributing genetically-modified organisms (GMOs), as well as export and import regulations. Our analysis reveals that important components of the ATT kit are freely available for research purposes but not or only with considerable effort for commercial use and distribution. We conclude with a number of considerations and requirements that need to be met in order to successfully disseminate such a kit in the future.
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Affiliation(s)
- Holger Spiegel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- *Correspondence: Holger Spiegel,
| | - Greta Nölke
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Harry Thangaraj
- Independent Consultant, (Residential Address Withheld), Finchley, London, United Kingdom
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Justus-Liebig-Universität Giessen, Department of Phytopathology, Giessen, Germany
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14
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Shang K, Xu Y, Cao W, Xie X, Zhang Y, Zhang J, Liu H, Zhou S, Zhu X, Zhu C. Potato (Solanum tuberosum L.) non-specific lipid transfer protein StLTP6 promotes viral infection by inhibiting virus-induced RNA silencing. PLANTA 2022; 256:54. [PMID: 35927530 DOI: 10.1007/s00425-022-03948-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
For the first time it is reported that members of the nsLTP protein family could promote viral infection by inhibiting virus-induced RNA silencing. Non-specific lipid transfer proteins (nsLTPs) are a class of soluble proteins with low relative molecular weight and widely present in higher plants. The role of nsLTPs in biotic and abiotic stresses has been studied, but no report has shown that nsLTPs play a role in the process of viral infection. We report the function and mechanism of the classical nsLTP protein StLTP6 in viral infection. We found that StLTP6 expression was remarkably upregulated in potato infected with potato virus Y and potato virus S. The infection efficiency and virus content of StLTP6-overexpressed potato and Nicotiana benthamiana were remarkable increased. Further study found that the overexpression of StLTP6 inhibited the expression of multiple genes in the RNA silencing pathway, thereby inhibiting virus-induced RNA silencing. This result indicated that StLTP6 expression was induced during viral infection to inhibit the resistance of virus-induced RNA silencing and promote viral infection. In summary, we reported the role of StLTP6 in viral infection, broadening the biological function range of the nsLTP family and providing valuable information for the study of viral infection mechanism.
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Affiliation(s)
- Kaijie Shang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yang Xu
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, 266100, China
| | - Weilin Cao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xiaoying Xie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yanru Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Jingfeng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Hongmei Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Shumei Zhou
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xiaoping Zhu
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Changxiang Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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15
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Imran M, Liu T, Wang Z, Wang M, Liu S, Gao X, Wang A, Liu S, Tian Z, Zhang M. Evolutionary conservation of nested MIR159 structural microRNA genes and their promoter characterization in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:948751. [PMID: 35958213 PMCID: PMC9361848 DOI: 10.3389/fpls.2022.948751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs, that are vital for gene expression regulation in eukaryotes. Whenever a pri-miRNA precursor includes another miRNA precursor, and both of these precursors may generate independent, non-overlapping mature miRNAs, we named them nested miRNAs. However, the extent of nested miR159 structural evolutionary conservation and its promoter characterization remains unknown. In this study, the sequence alignment and phylogenetic analysis reveal that the MIR159 family is ancient, and its nested miR159 structures are evolutionary conserved in different plant species. The overexpression of ath-MIR159a, including the 1.2 kb downstream region, has no effect on rescuing the mir159ab phenotype. The promoter truncation results revealed that the 1.0 kb promoter of ath-MIR159a is sufficient for rescuing the mir159ab phenotype. The cis-regulatory elements in the ath-miR159a promoters indicated functions related to different phytohormones, abiotic stresses, and transcriptional activation. While the MybSt1 motif-containing region is not responsible for activating the regulation of the miR159a promoter. The qRT-PCR results showed that overexpression of ath-MIR159a led to high expression levels of miR159a.1-5 and miR159a.1-3 and complemented the growth defect of mir159ab via downregulation of MYB33 and MYB65. Furthermore, continuously higher expression of the miR159a.2 duplex in transgenic lines with the curly leaf phenotype indicates that miR159a.2 is functional in Arabidopsis and suggests that it is possible for a miRNA precursor to encode several regulatory small RNAs in plants. Taken together, our study demonstrates that the nested miR159 structure is evolutionary conserved and miRNA-mediated gene regulation is more complex than previously thought.
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Affiliation(s)
- Muhammad Imran
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Tengfei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zheng Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
| | - Min Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xinyan Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Anning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Songfeng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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16
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Imran M, Liu T, Wang Z, Wang M, Liu S, Gao X, Wang A, Liu S, Tian Z, Zhang M. Nested miRNA Secondary Structure Is a Unique Determinant of miR159 Efficacy in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:905264. [PMID: 35720551 PMCID: PMC9201385 DOI: 10.3389/fpls.2022.905264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are 20- to 24-nucleotide small RNAs, and whenever a pri-miRNA precursor includes another miRNA precursor, and both of these precursors may generate independent non overlapping mature miRNAs, we called them nested miRNAs. However, the functional and regulatory roles of nested miRNA structures in plants are still unknown. In this study, the Arabidopsis nested miR159a structure, which consists of two nested miRNAs, miR159a.1, and miR159a.2, was used as a model to determine miRNA-mediated gene silencing in plants. Complementation analysis of nested miR159a structures revealed that the miR159a structure can differentially complement the mir159ab phenotype, and a duplex nested structure in the tail end region of the pre-miR159a fold back may have a possible dominant function, indicating the importance of the flanking sequence of the stem in the cleavage of the mature miRNA. Furthermore, continuously higher expression of the miR159a.2 duplex in the severe leaf curl phenotype indicates that miR159a.2 is functional in Arabidopsis and suggests that in plants, a miRNA precursor may encode multiple regulatory small RNAs. Taken together, our study demonstrates that the nested miR159a structure regulated by duplex mutations of miR159a has a unique pattern and provides novel insight into silencing efficacy of Arabidopsis miR159a.
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Affiliation(s)
- Muhammad Imran
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Tengfei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zheng Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
| | - Min Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xinyan Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Anning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Songfeng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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17
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Singer K, Lee LY, Yuan J, Gelvin SB. Characterization of T-Circles and Their Formation Reveal Similarities to Agrobacterium T-DNA Integration Patterns. FRONTIERS IN PLANT SCIENCE 2022; 13:849930. [PMID: 35599900 PMCID: PMC9121065 DOI: 10.3389/fpls.2022.849930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Agrobacterium transfers T-DNA to plants where it may integrate into the genome. Non-homologous end-joining (NHEJ) has been invoked as the mechanism of T-DNA integration, but the role of various NHEJ proteins remains controversial. Genetic evidence for the role of NHEJ in T-DNA integration has yielded conflicting results. We propose to investigate the formation of T-circles as a proxy for understanding T-DNA integration. T-circles are circular double-strand T-DNA molecules, joined at their left (LB) and right (RB) border regions, formed in plants. We characterized LB-RB junction regions from hundreds of T-circles formed in Nicotiana benthamiana or Arabidopsis thaliana. These junctions resembled T-DNA/plant DNA junctions found in integrated T-DNA: Among complex T-circles composed of multiple T-DNA molecules, RB-RB/LB-LB junctions predominated over RB-LB junctions; deletions at the LB were more frequent and extensive than those at the RB; microhomology was frequently used at junction sites; and filler DNA, from the plant genome or various Agrobacterium replicons, was often present between the borders. Ku80 was not required for efficient T-circle formation, and a VirD2 ω mutation affected T-circle formation and T-DNA integration similarly. We suggest that investigating the formation of T-circles may serve as a surrogate for understanding T-DNA integration.
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18
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Ishihama N, Laohavisit A, Takizawa K, Shirasu K. Apoplastic Expression of CARD1-ecto Domain in Nicotiana benthamiana and Purification from the Apoplastic Fluids. Bio Protoc 2022; 12:e4387. [PMID: 35800094 PMCID: PMC9081474 DOI: 10.21769/bioprotoc.4387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 12/16/2021] [Accepted: 03/06/2022] [Indexed: 12/29/2022] Open
Abstract
The protein expression and purification process is an essential initial step for biochemical analysis of a protein of interest. Traditionally, heterologous protein expression systems (such as E. coli, yeast, insect cells, and cell-free) are employed for plant protein expression, although a plant expression system is often desirable for plant proteins, to ensure proper post-translational modifications. Here, we describe a method to express and purify the ectodomain of one of the leucine-rich repeat receptor-like kinase called CARD1/HPCA1, from Nicotiana benthamiana apoplastic fluid. First, we express His-tagged CARD1 ectodomain in the apoplastic space of N. benthamiana by the Agroinfiltration method. Then, we collect apoplastic fluids from the leaves and purify the His-tagged protein by Ni2+-affinity chromatography. In addition to plant-specific post-translational modifications, protein accumulated in the plant apoplastic space, rather than in the cytosolic space, should be kept under an oxidizing environment. Such an environment will help to maintain the property of intrinsic disulfide bonds in the protein of interest. Further, purification from the apoplastic fluids, rather than the total protein extract, will significantly reduce contaminants (for instance RuBisCO) during protein extraction, and simplify downstream processes. We envisage that our system will be useful for expressing various plant proteins, particularly the apoplastic or extracellular regions of membrane proteins.
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Affiliation(s)
| | | | - Kaori Takizawa
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
,Graduate School of Science, The University of Tokyo, Bunkyo, Japan
,
*For correspondence:
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19
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Development of Plant-Based Vaccines for Prevention of Avian Influenza and Newcastle Disease in Poultry. Vaccines (Basel) 2022; 10:vaccines10030478. [PMID: 35335110 PMCID: PMC8952014 DOI: 10.3390/vaccines10030478] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023] Open
Abstract
Viral diseases, including avian influenza (AI) and Newcastle disease (ND), are an important cause of morbidity and mortality in poultry, resulting in significant economic losses. Despite the availability of commercial vaccines for the major viral diseases of poultry, these diseases continue to pose a significant risk to global food security. There are multiple factors for this: vaccine costs may be prohibitive, cold chain storage for attenuated live-virus vaccines may not be achievable, and commercial vaccines may protect poorly against local emerging strains. The development of transient gene expression systems in plants provides a versatile and robust tool to generate a high yield of recombinant proteins with superior speed while managing to achieve cost-efficient production. Plant-derived vaccines offer good stability and safety these include both subunit and virus-like particle (VLP) vaccines. VLPs offer potential benefits compared to currently available traditional vaccines, including significant reductions in virus shedding and the ability to differentiate between infected and vaccinated birds (DIVA). This review discusses the current state of plant-based vaccines for prevention of the AI and ND in poultry, challenges in their development, and potential for expanding their use in low- and middle-income countries.
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20
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Spies FP, Raineri J, Miguel VN, Cho Y, Hong JC, Chan RL. The Arabidopsis transcription factors AtPHL1 and AtHB23 act together promoting carbohydrate transport from pedicel-silique nodes to seeds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111133. [PMID: 35067303 DOI: 10.1016/j.plantsci.2021.111133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/29/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Carbohydrates are produced in green tissues through photosynthesis and then transported to sink tissues. Carbon partitioning is a strategic process, fine regulated, involving specific sucrose transporters in each connecting tissue. Here we report that a screening of an Arabidopsis transcription factor (TF) library using the homeodomain-leucine zipper I member AtHB23 as bait, allowed identifying the TF AtPHL1 interacting with the former. An independent Y2H assay, and in planta by BiFC, confirmed such interaction. AtHB23 and AtPHL1 coexpressed in the pedicel-silique nodes and the funiculus. Mutant plants (phl1, and amiR23) showed a marked reduction of lipid content in seeds, although lipid composition did not change compared to the wild type. While protein and carbohydrate contents were not significantly different between mutants and control mature seeds, we observed a reduced carbohydrate content in mutant plants young siliques (7 days after pollination). Moreover, using a CFDA probe, we revealed an impaired transport to the seeds, and the gene encoding the carbohydrate transporters SWEET10 and SWEET11, usually expressed in connecting tissues, was repressed in the amiR23 and phl1 mutant plants. Altogether, the results indicated that AtHB23 and AtPHL1 act together, promoting sucrose transport, and the lack of any of them provoked a reduction in seeds lipid content.
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Affiliation(s)
- Fiorella Paola Spies
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
| | - Jesica Raineri
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
| | - Virginia Natalí Miguel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
| | - Yuhan Cho
- Division of Life Science, Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea.
| | - Jong Chan Hong
- Division of Life Science, Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea; Division of Plant Sciences, University of Missouri, Columbia, MO, 65211-7310, USA.
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
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21
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Development of a new recombineering system for Agrobacterium species. Appl Environ Microbiol 2022; 88:e0249921. [PMID: 35044833 DOI: 10.1128/aem.02499-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discovery of new and efficient genetic engineering technologies for Agrobacterium will broaden the capacity for fundamental research on this genus and for its utilization as a transgenic vehicle. In this study, we aim to develop an efficient recombineering system for Agrobacterium species. We examined isolates of Agrobacterium and the closely related genus Rhizobium to identify pairs of ET-like recombinases that would aid in the recombineering of Agrobacterium species. Four pairs of ET-like recombinases, named RecETh1h2h3h4AGROB6, RecETh1h2P3RHI597, RecETRHI145, and RecEThRHI483, were identified in Agrobacterium tumefaciens str. B6, Rhizobium leguminosarum bv. trifolii WSM597, Rhizobium sp. LC145, and Rhizobium sp. Root483D2, respectively. Eight more candidate recombineering systems were generated by combining the new ET-like recombinases with Redγ or Pluγ. The PluγETRHI145 system, RecETh1h2h3h4AGROB6 system, and PluγEThRHI483 system were determined to be the most efficient recombineering system for the type strains A. tumefaciens C58, A. tumefaciens EHA105, and R. rhizogenes NBCR13257, respectively. The utility of these systems was demonstrated by knocking out the istB and istA fusion gene in C58, the celI gene in EHA105, and the 3'-5' exonuclease gene and endoglucanase gene in NBCR13257. Our work provides an effective genetic manipulation strategy for Agrobacterium species. IMPORTANCE Agrobacterium is a powerful transgenic vehicle for the genetic manipulation of numerous plant and fungal species and even animal cells. In addition to improving the utility of Agrobacterium as a transgenic vehicle, genetic engineering tools are important for revealing crucial components that are functionally involved in T-DNA translocation events. This work developed an efficient and versatile recombineering system for Agrobacterium. Successful genome modification of Agrobacterium strains revealed that this new recombineering system could be used for the genetic engineering of Agrobacterium.
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22
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Chou L, Lin YC, Haryono M, Santos MNM, Cho ST, Weisberg AJ, Wu CF, Chang JH, Lai EM, Kuo CH. Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol 2022; 20:16. [PMID: 35022048 PMCID: PMC8756689 DOI: 10.1186/s12915-021-01221-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Many named species as defined in current bacterial taxonomy correspond to species complexes. Uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized the Agrobacterium tumefaciens species complex (a.k.a. Agrobacterium biovar 1), a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes. RESULTS We utilized 35 genome assemblies, including 14 newly generated ones, to achieve a phylogenetically balanced sampling of A. tumefaciens. Our genomic analysis suggested that the 10 genomospecies described previously are distinct biological species and supported a quantitative guideline for species delineation. Furthermore, our inference of gene content and core-genome phylogeny allowed for investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins. CONCLUSIONS We demonstrate that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. We show that the T6SS VgrG proteins involved in specific effector binding and delivery can be classified into distinct types based on domain organization. The co-occurrence patterns of VgrG-associated domains and the neighboring genes that encode different chaperones/effectors can be used to infer possible interacting partners. Similarly, the associations between plant host preference and the pTi type among these strains can be used to infer phenotype-genotype correspondence. Our strategies for multi-level investigations at scales that range from whole genomes to intragenic domains and phylogenetic depths from between- to within-species are applicable to other bacteria. Furthermore, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.
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Affiliation(s)
- Lin Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mary Nia M Santos
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Chih-Feng Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan. .,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan. .,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
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23
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Nahirñak V, Almasia NI, González MN, Massa GA, Décima Oneto CA, Feingold SE, Hopp HE, Vazquez Rovere C. State of the Art of Genetic Engineering in Potato: From the First Report to Its Future Potential. FRONTIERS IN PLANT SCIENCE 2022; 12:768233. [PMID: 35082806 PMCID: PMC8784693 DOI: 10.3389/fpls.2021.768233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Potato (Solanum tuberosum L.) is a crop of world importance that produces tubers of high nutritional quality. It is considered one of the promising crops to overcome the challenges of poverty and hunger worldwide. However, it is exposed to different biotic and abiotic stresses that can cause significant losses in production. Thus, potato is a candidate of special relevance for improvements through conventional breeding and biotechnology. Since conventional breeding is time-consuming and challenging, genetic engineering provides the opportunity to introduce/switch-off genes of interest without altering the allelic combination that characterize successful commercial cultivars or to induce targeted sequence modifications by New Breeding Techniques. There is a variety of methods for potato improvement via genetic transformation. Most of them incorporate genes of interest into the nuclear genome; nevertheless, the development of plastid transformation protocols broadened the available approaches for potato breeding. Although all methods have their advantages and disadvantages, Agrobacterium-mediated transformation is the most used approach. Alternative methods such as particle bombardment, protoplast transfection with polyethylene glycol and microinjection are also effective. Independently of the DNA delivery approach, critical steps for a successful transformation are a rapid and efficient regeneration protocol and a selection system. Several critical factors affect the transformation efficiency: vector type, insert size, Agrobacterium strain, explant type, composition of the subculture media, selective agent, among others. Moreover, transient or stable transformation, constitutive or inducible promoters, antibiotic/herbicide resistance or marker-free strategies can be considered. Although great efforts have been made to optimize all the parameters, potato transformation protocols are highly genotype-dependent. Genome editing technologies provide promising tools in genetic engineering allowing precise modification of targeted sequences. Interestingly, transient expression of genome editing components in potato protoplasts was reported to generate edited plants without the integration of any foreign DNA, which is a valuable aspect from both a scientific and a regulatory perspective. In this review, current challenges and opportunities concerning potato genetic engineering strategies developed to date are discussed. We describe their critical parameters and constrains, and the potential application of the available tools for functional analyses or biotechnological purposes. Public concerns and safety issues are also addressed.
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Affiliation(s)
- Vanesa Nahirñak
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Natalia I. Almasia
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Matías N. González
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
| | - Gabriela A. Massa
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Cecilia A. Décima Oneto
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Sergio E. Feingold
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
| | - Horacio E. Hopp
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cecilia Vazquez Rovere
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
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24
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Quantifying Plasmodesmatal Transport with an Improved GFP Movement Assay. Methods Mol Biol 2022; 2457:285-298. [PMID: 35349148 PMCID: PMC9875380 DOI: 10.1007/978-1-0716-2132-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Plasmodesmata (PD) are membrane-lined channels that cross the cell wall to connect the cytosol of adjacent plant cells, permitting diverse cytosolic molecules to move between cells. PD are essential for plant multicellularity, and the regulation of PD transport contributes to metabolism, developmental patterning, abiotic stress responses, and pathogen defenses, which has sparked broad interest in PD among diverse plant biologists. Here, we present a straightforward method to reproducibly quantify changes in the rate of PD transport in leaves. Individual cells are transformed with Agrobacterium to express fluorescent proteins, which then move beyond the transformed cell via PD. Forty-eight to 72 h later, the extent of GFP movement is monitored by confocal fluorescence microscopy. This assay is versatile and may be combined with transient gene overexpression, virus-induced gene silencing, physiological treatments, or pharmaceutical treatments to test how PD transport responds to specific conditions. We expect that this improved method for monitoring PD transport in leaves will be broadly useful for plant biologists working in diverse fields.
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25
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Wu HY, Lai EM. AGROBEST: A Highly Efficient Agrobacterium-Mediated Transient Expression System in Arabidopsis Seedlings. Methods Mol Biol 2022; 2379:113-123. [PMID: 35188659 DOI: 10.1007/978-1-0716-1791-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Agrobacterium-mediated transient transformation for gene expression is a simple and fast method to analyze transgene functions in plants. Agroinfiltration in leaves of Nicotiana benthamiana is a common method for transient expression. However, agroinfiltration in leaves of Arabidopsis thaliana is challenging due to the low and variable efficiency. Here, we describe procedures of a highly efficient and robust Agrobacterium-mediated transient expression system, named AGROBEST (Agrobacterium-mediated enhanced seedling transformation) for gene expression in A. thaliana seedlings. High efficiency of AGROBEST has been achieved by virulence (vir) gene pre-induction of a specific disarmed Agrobacterium tumefaciens strain C58C1(pTiB6S3ΔT)H followed by co-cultivation with Arabidopsis seedlings in an optimized medium with AB salts and buffered acidic plant culture medium. The stable acidic medium largely increases Agrobacterium-mediated transient expression levels and reduces plant defense responses, suggesting that AGROBEST enables high transient expression efficiency by compromising plant immunity. In summary, AGROBEST is a simple, fast, reliable, and robust transient expression system offering a quick and convenient method to observe protein localization, protein-protein interactions, promoter activities, and gene functional studies in Arabidopsis seedlings.
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Affiliation(s)
- Hung-Yi Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
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26
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Alok A, Chauhan H, Upadhyay SK, Pandey A, Kumar J, Singh K. Compendium of Plant-Specific CRISPR Vectors and Their Technical Advantages. Life (Basel) 2021; 11:1021. [PMID: 34685392 PMCID: PMC8540340 DOI: 10.3390/life11101021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/25/2022] Open
Abstract
CRISPR/Cas mediated genome editing is a revolutionary approach for manipulating the plant genome. However, the success of this technology is highly dependent on selection of a specific vector and the other components. A plant-specific CRISPR/Cas vector usually consists of a Cas gene, target-specific gRNA, leader sequence, selectable marker gene, precise promoters, and other accessories. It has always been challenging to select the specific vector for each study due to a lack of comprehensive information on CRISPR vectors in one place. Herein, we have discussed every technical aspect of various important elements that will be highly useful in vector selection and efficient editing of the desired plant genome. Various factors such as the promoter regulating the expression of Cas and gRNA, gRNA size, Cas variants, multicistronic gRNA, and vector backbone, etc. influence transformation and editing frequency. For example, the use of polycistronic tRNA-gRNA, and Csy4-gRNA has been documented to enhance the editing efficiency. Similarly, the selection of an efficient selectable marker is also a very important factor. Information on the availability of numerous variants of Cas endonucleases, such as Cas9, Cas12a, Cas12b, Casɸ, and CasMINI, etc., with diverse recognition specificities further broadens the scope of editing. The development of chimeric proteins such as Cas fused to cytosine or adenosine deaminase domain and modified reverse transcriptase using protein engineering enabled base and prime editing, respectively. In addition, the newly discovered Casɸ and CasMINI would increase the scope of genetic engineering in plants by being smaller Cas variants. All advancements would contribute to the development of various tools required for gene editing, targeted gene insertion, transcriptional activation/suppression, multiplexing, prime editing, base editing, and gene tagging. This review will serve as an encyclopedia for plant-specific CRISPR vectors and will be useful for researchers.
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Affiliation(s)
- Anshu Alok
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; (A.A.); (H.C.)
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Hanny Chauhan
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; (A.A.); (H.C.)
| | | | - Ashutosh Pandey
- National Institute of Plant Genome Research, New Delhi 110067, India;
| | - Jitendra Kumar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; (A.A.); (H.C.)
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27
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Savage Z, Duggan C, Toufexi A, Pandey P, Liang Y, Segretin ME, Yuen LH, Gaboriau DCA, Leary AY, Tumtas Y, Khandare V, Ward AD, Botchway SW, Bateman BC, Pan I, Schattat M, Sparkes I, Bozkurt TO. Chloroplasts alter their morphology and accumulate at the pathogen interface during infection by Phytophthora infestans. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1771-1787. [PMID: 34250673 DOI: 10.1111/tpj.15416] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 05/22/2023]
Abstract
Upon immune activation, chloroplasts switch off photosynthesis, produce antimicrobial compounds and associate with the nucleus through tubular extensions called stromules. Although it is well established that chloroplasts alter their position in response to light, little is known about the dynamics of chloroplast movement in response to pathogen attack. Here, we report that during infection with the Irish potato famine pathogen Phytophthora infestans, chloroplasts accumulate at the pathogen interface, associating with the specialized membrane that engulfs the pathogen haustorium. The chemical inhibition of actin polymerization reduces the accumulation of chloroplasts at pathogen haustoria, suggesting that this process is partially dependent on the actin cytoskeleton. However, chloroplast accumulation at haustoria does not necessarily rely on movement of the nucleus to this interface and is not affected by light conditions. Stromules are typically induced during infection, embracing haustoria and facilitating chloroplast interactions, to form dynamic organelle clusters. We found that infection-triggered stromule formation relies on BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1)-mediated surface immune signaling, whereas chloroplast repositioning towards haustoria does not. Consistent with the defense-related induction of stromules, effector-mediated suppression of BAK1-mediated immune signaling reduced stromule formation during infection. On the other hand, immune recognition of the same effector stimulated stromules, presumably via a different pathway. These findings implicate chloroplasts in a polarized response upon pathogen attack and point to more complex functions of these organelles in plant-pathogen interactions.
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Affiliation(s)
- Zachary Savage
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Cian Duggan
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Alexia Toufexi
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Pooja Pandey
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Yuxi Liang
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - María Eugenia Segretin
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular 'Dr Héctor N. Torres' (INGEBI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Vuelta de Obligado 2490, Ciudad Autónoma de Buenos Aires, C1428ADN, Argentina
| | - Lok Him Yuen
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - David C A Gaboriau
- Facility for Imaging by Light Microscopy, Faculty of Medicine, National Heart & Lung Institute (NHLI), Imperial College London, South Kensington, SAF building, London, SW7 2AZ, UK
| | - Alexandre Y Leary
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Yasin Tumtas
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Virendrasinh Khandare
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
| | - Andrew D Ward
- Central Laser Facility, Science and Technology Facilities Council Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0QX, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0QX, UK
| | - Benji C Bateman
- Central Laser Facility, Science and Technology Facilities Council Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0QX, UK
| | - Indranil Pan
- Centre for Process Systems Engineering and Centre for Environmental Policy, Imperial College London, South Kensington Campus, London, London, SW7 2AZ, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London, London, NW1 2DB, UK
| | - Martin Schattat
- Martin Luther Universität Halle-Wittenberg, Halle, 06108 Halle, Germany
| | - Imogen Sparkes
- School of Biological Sciences, University of Bristol, University of Bristol, St Michael's Hill, Bristol, BS8 8DZ, UK
| | - Tolga O Bozkurt
- Department of Life Sciences, Imperial College London, Imperial College Road, South Kensington Campus, London, London, SW7 2AZ, UK
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28
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Mills A, Jaganatha V, Cortez A, Guzman M, Burnette JM, Collin M, Lopez-Lopez B, Wessler SR, Van Norman JM, Nelson DC, Rasmussen CG. A Course-Based Undergraduate Research Experience in CRISPR-Cas9 Experimental Design to Support Reverse Genetic Studies in Arabidopsis thaliana. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:e00155-21. [PMID: 34594454 PMCID: PMC8442021 DOI: 10.1128/jmbe.00155-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Gene-editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene-editing technology as well as develop their soft skills in data management and scientific communication. We present two versions of the course that can be implemented with twice-weekly meetings over a 5-week period. In the remote-learning version, students performed homology searches, designed guide RNAs (gRNAs) and primers, and learned the principles of molecular cloning. This version is appropriate when access to laboratory equipment or in-person instruction is limited, such as during closures that have occurred in response to the COVID-19 pandemic. In person, students designed gRNAs, cloned CRISPR-Cas9 constructs, and performed genetic transformation of Arabidopsis thaliana. Students learned how to design effective gRNA pairs targeting their assigned gene with an 86% success rate. Final exams tested students' ability to apply knowledge of an unfamiliar genome database to characterize gene structure and to properly design gRNAs. Average final exam scores of ∼73% and ∼84% for in-person and remote-learning CUREs, respectively, indicated that students met learning outcomes. The highly parallel nature of the CURE makes it possible to target dozens to hundreds of genes, depending on the number of sections. Applying this approach in a sensitized mutant background enables focused reverse genetic screens for genetic suppressors or enhancers. The course can be adapted readily to other organisms or projects that employ gene editing.
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Affiliation(s)
- Alison Mills
- Biochemistry and Molecular Biology Graduate Program, University of California, Riverside, California, USA
| | - Venkateswari Jaganatha
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Alejandro Cortez
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Michael Guzman
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - James M. Burnette
- College of Natural and Agricultural Sciences, University of California, Riverside, California, USA
| | - Matthew Collin
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Berenise Lopez-Lopez
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Susan R. Wessler
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Jaimie M. Van Norman
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - David C. Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Carolyn G. Rasmussen
- Biochemistry and Molecular Biology Graduate Program, University of California, Riverside, California, USA
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
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29
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Tuo D, Zhou P, Yan P, Cui H, Liu Y, Wang H, Yang X, Liao W, Sun D, Li X, Shen W. A cassava common mosaic virus vector for virus-induced gene silencing in cassava. PLANT METHODS 2021; 17:74. [PMID: 34247636 PMCID: PMC8273954 DOI: 10.1186/s13007-021-00775-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/01/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cassava is an important crop for food security and industry in the least-developed and developing countries. The completion of the cassava genome sequence and identification of large numbers of candidate genes by next-generation sequencing provide extensive resources for cassava molecular breeding and increase the need for rapid and efficient gene function analysis systems in cassava. Several plant virus-induced gene silencing (VIGS) systems have been developed as reverse genetic tools for rapid gene function analysis in cassava. However, these VIGS vectors could cause severe viral symptoms or inefficient gene silencing. RESULTS In this study, we constructed agroinfection-compatible infectious cDNA clones of cassava common mosaic virus isolate CM (CsCMV-CM, genus Potexvirus, family Alphaflexiviridae) that causes systemic infection with mild symptoms in cassava. CsCMV-CM was then modified to a viral vector carrying the Nimble cloning frame, which facilitates the rapid and high-throughput cloning of silencing fragments into the viral genome. The CsCMV-based vector successfully silenced phytoene desaturase (PDS) and magnesium chelatase subunit I (ChlI) in different cassava varieties and Nicotiana benthamiana. The silencing of the ChlI gene could persist for more than two months. CONCLUSIONS This CsCMV-based VIGS system provides a new tool for rapid and efficient gene function studies in cassava.
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Affiliation(s)
- Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hongguang Cui
- College of Plant Protection, Hainan University, Haikou, 570228, China
| | - Yang Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- College of Horticulture, Hainan University, Haikou, 570228, China
| | - He Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- College of Horticulture, Hainan University, Haikou, 570228, China
| | - Xiukun Yang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- College of Horticulture, Hainan University, Haikou, 570228, China
| | - Wenbin Liao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Di Sun
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- College of Horticulture, Hainan University, Haikou, 570228, China
| | - Xiaoying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources &, Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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D’Incà E, Cazzaniga S, Foresti C, Vitulo N, Bertini E, Galli M, Gallavotti A, Pezzotti M, Battista Tornielli G, Zenoni S. VviNAC33 promotes organ de-greening and represses vegetative growth during the vegetative-to-mature phase transition in grapevine. THE NEW PHYTOLOGIST 2021; 231:726-746. [PMID: 33567124 PMCID: PMC8251598 DOI: 10.1111/nph.17263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/01/2021] [Indexed: 05/08/2023]
Abstract
Plants undergo several developmental transitions during their life cycle. In grapevine, a perennial woody fruit crop, the transition from vegetative/green-to-mature/woody growth involves transcriptomic reprogramming orchestrated by a small group of genes encoding regulators, but the underlying molecular mechanisms are not fully understood. We investigated the function of the transcriptional regulator VviNAC33 by generating and characterizing transgenic overexpressing grapevine lines and a chimeric repressor, and by exploring its putative targets through a DNA affinity purification sequencing (DAP-seq) approach combined with transcriptomic data. We demonstrated that VviNAC33 induces leaf de-greening, inhibits organ growth and directly activates the expression of STAY-GREEN PROTEIN 1 (SGR1), which is involved in Chl and photosystem degradation, and AUTOPHAGY 8f (ATG8f), which is involved in the maturation of autophagosomes. Furthermore, we show that VviNAC33 directly inhibits AUXIN EFFLUX FACILITATOR PIN1, RopGEF1 and ATP SYNTHASE GAMMA CHAIN 1T (ATPC1), which are involved in photosystem II integrity and activity. Our results show that VviNAC33 plays a major role in terminating photosynthetic activity and organ growth as part of a regulatory network governing the vegetative-to-mature phase transition.
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Affiliation(s)
- Erica D’Incà
- Department of BiotechnologyUniversity of VeronaVerona37134Italy
| | | | - Chiara Foresti
- Department of BiotechnologyUniversity of VeronaVerona37134Italy
| | - Nicola Vitulo
- Department of BiotechnologyUniversity of VeronaVerona37134Italy
| | - Edoardo Bertini
- Department of BiotechnologyUniversity of VeronaVerona37134Italy
| | - Mary Galli
- Waksman Institute of MicrobiologyRutgers UniversityPiscatawayNJ08854‐8020USA
| | - Andrea Gallavotti
- Waksman Institute of MicrobiologyRutgers UniversityPiscatawayNJ08854‐8020USA
| | - Mario Pezzotti
- Department of BiotechnologyUniversity of VeronaVerona37134Italy
| | | | - Sara Zenoni
- Department of BiotechnologyUniversity of VeronaVerona37134Italy
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Mishra LS, Mishra S, Caddell DF, Coleman-Derr D, Funk C. The Plastid-Localized AtFtsHi3 Pseudo-Protease of Arabidopsis thaliana Has an Impact on Plant Growth and Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2021; 12:694727. [PMID: 34249066 PMCID: PMC8261292 DOI: 10.3389/fpls.2021.694727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/28/2021] [Indexed: 05/22/2023]
Abstract
While drought severely affects plant growth and crop production, the molecular mechanisms of the drought response of plants remain unclear. In this study, we demonstrated for the first time the effect of the pseudo-protease AtFtsHi3 of Arabidopsis thaliana on overall plant growth and in drought tolerance. An AtFTSHi3 knock-down mutant [ftshi3-1(kd)] displayed a pale-green phenotype with lower photosynthetic efficiency and Darwinian fitness compared to wild type (Wt). An observed delay in seed germination of ftshi3-1(kd) was attributed to overaccumulation of abscisic acid (ABA); ftshi3-1(kd) seedlings showed partial sensitivity to exogenous ABA. Being exposed to similar severity of soil drying, ftshi3-1(kd) was drought-tolerant up to 20 days after the last irrigation, while wild type plants wilted after 12 days. Leaves of ftshi3-1(kd) contained reduced stomata size, density, and a smaller stomatic aperture. During drought stress, ftshi3-1(kd) showed lowered stomatal conductance, increased intrinsic water-use efficiency (WUEi), and slower stress acclimation. Expression levels of ABA-responsive genes were higher in leaves of ftshi3-1(kd) than Wt; DREB1A, but not DREB2A, was significantly upregulated during drought. However, although ftshi3-1(kd) displayed a drought-tolerant phenotype in aboveground tissue, the root-associated bacterial community responded to drought.
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Affiliation(s)
| | - Sanatkumar Mishra
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Daniel F. Caddell
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA, United States
| | - Devin Coleman-Derr
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
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32
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Mielke K, Wagner R, Mishra LS, Demir F, Perrar A, Huesgen PF, Funk C. Abundance of metalloprotease FtsH12 modulates chloroplast development in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3455-3473. [PMID: 33216923 PMCID: PMC8042743 DOI: 10.1093/jxb/eraa550] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/19/2020] [Indexed: 05/11/2023]
Abstract
The ATP-dependent metalloprotease FtsH12 (filamentation temperature sensitive protein H 12) has been suggested to participate in a heteromeric motor complex, driving protein translocation into the chloroplast. FtsH12 was immuno-detected in proplastids, seedlings, leaves, and roots. Expression of Myc-tagged FtsH12 under its native promotor allowed identification of FtsHi1, 2, 4, and 5, and plastidic NAD-malate dehydrogenase, five of the six interaction partners in the suggested import motor complex. Arabidopsis thaliana mutant seedlings with reduced FTSH12 abundance exhibited pale cotyledons and small, deformed chloroplasts with altered thylakoid structure. Mature plants retained these chloroplast defects, resulting in slightly variegated leaves and lower chlorophyll content. Label-free proteomics revealed strong changes in the proteome composition of FTSH12 knock-down seedlings, reflecting impaired plastid development. The composition of the translocon on the inner chloroplast membrane (TIC) protein import complex was altered, with coordinated reduction of the FtsH12-FtsHi complex subunits and accumulation of the 1 MDa TIC complex subunits TIC56, TIC214 and TIC22-III. FTSH12 overexpressor lines showed no obvious phenotype, but still displayed distinct differences in their proteome. N-terminome analyses further demonstrated normal proteolytic maturation of plastid-imported proteins irrespective of FTSH12 abundance. Together, our data suggest that FtsH12 has highest impact during seedling development; its abundance alters the plastid import machinery and impairs chloroplast development.
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Affiliation(s)
- Kati Mielke
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Raik Wagner
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, Jülich, Germany
| | - Andreas Perrar
- Central Institute for Engineering, Electronics and Analytics, Jülich, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
- Institute of Biochemistry, University of Cologne, Cologne, Germany
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33
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Park SI, Kim HB, Jeon HJ, Kim H. Agrobacterium-Mediated Capsicum annuum Gene Editing in Two Cultivars, Hot Pepper CM334 and Bell Pepper Dempsey. Int J Mol Sci 2021; 22:3921. [PMID: 33920210 PMCID: PMC8070316 DOI: 10.3390/ijms22083921] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022] Open
Abstract
Peppers (Capsicum annuum L.) are the most widespread and cultivated species of Solanaceae in subtropical and temperate countries. These vegetables are economically attractive worldwide. Although whole-genome sequences of peppers and genome-editing tools are currently available, the precision editing of peppers is still in its infancy because of the lack of a stable pepper transformation method. Here, we employed three Agrobacterium tumefaciens strains-AGL1, EHA101, and GV3101-to investigate which Agrobacterium strain could be used for pepper transformation. Hot pepper CM334 and bell pepper Dempsey were chosen in this study. Agrobacterium tumefaciens GV3101 induced the highest number of calli in cv. Dempsey. All three strains generated similar numbers of calli for cv. CM334. We optimized a suitable concentration of phosphinothricin (PPT) to select a CRISPR/Cas9 binary vector (pBAtC) for both pepper types. Finally, we screened transformed calli for PPT resistance (1 and 5 mg/L PPT for cv. CM334 and Dempsey, respectively). These selected calli showed different indel frequencies from the non-transformed calli. However, the primary indel pattern was consistent with a 1-bp deletion at the target locus of the C. annuumMLO gene (CaMLO2). These results demonstrate the different sensitivity between cv. CM334 and Dempsey to A. tumefaciens-mediated callus induction, and a differential selection pressure of PPT via pBAtC binary vector.
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Affiliation(s)
- Sung-il Park
- Interdisciplinary Graduate Program in BIT Medical Convergence, Kangwon National University, Chuncheon 24341, Korea;
| | - Hyun-Bin Kim
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea; (H.-B.K.); (H.-J.J.)
| | - Hyun-Ji Jeon
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea; (H.-B.K.); (H.-J.J.)
| | - Hyeran Kim
- Interdisciplinary Graduate Program in BIT Medical Convergence, Kangwon National University, Chuncheon 24341, Korea;
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea; (H.-B.K.); (H.-J.J.)
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Wang C, Gao H, Chu Z, Ji C, Xu Y, Cao W, Zhou S, Song Y, Liu H, Zhu C. A nonspecific lipid transfer protein, StLTP10, mediates resistance to Phytophthora infestans in potato. MOLECULAR PLANT PATHOLOGY 2021; 22:48-63. [PMID: 33118686 PMCID: PMC7749752 DOI: 10.1111/mpp.13007] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 09/09/2020] [Accepted: 09/27/2020] [Indexed: 05/03/2023]
Abstract
Nonspecific lipidtransfer proteins (nsLTPs), which are small, cysteine-rich proteins, belong to the pathogenesis-related protein family, and several of them act as positive regulators during plant disease resistance. However, the underlying molecular mechanisms of these proteins in plant immune responses are unclear. In this study, a typical nsLTP gene, StLTP10, was identified and functionally analysed in potato. StLTP10 expression was significantly induced by Phytophthora infestans, which causes late blight in potato, and defence-related phytohormones, including abscisic acid (ABA), salicylic acid, and jasmonic acid. Characterization of StLTP10-overexpressing and knockdown lines indicated that StLTP10 positively regulates plant resistance to P. infestans. This resistance was coupled with enhanced expression of reactive oxygen species scavenging- and defence-related genes. Furthermore, we identified that StLTP10 physically interacts with ABA receptor PYL4 and affects its subcellular localization. These two proteins work together to regulate stomatal closure during pathogen infection. Interestingly, we also found that wound-induced protein kinase interacts with StLTP10 and positively regulates its protein abundance. Taken together, our results provide insight into the role of StLTP10 in resistance to P. infestans and suggest candidates to enhance broad-spectrum resistance to pathogens in potato.
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Affiliation(s)
- Chenchen Wang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’an, ShandongChina
| | - Hongjuan Gao
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’an, ShandongChina
| | - Zhaohui Chu
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai’an, ShandongChina
| | - Changquan Ji
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’an, ShandongChina
| | - Yang Xu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’an, ShandongChina
| | - Weilin Cao
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’an, ShandongChina
| | - Shumei Zhou
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’an, ShandongChina
| | - Yunzhi Song
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’an, ShandongChina
| | - Hongmei Liu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’an, ShandongChina
| | - Changxiang Zhu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai’an, ShandongChina
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De Saeger J, Park J, Chung HS, Hernalsteens JP, Van Lijsebettens M, Inzé D, Van Montagu M, Depuydt S. Agrobacterium strains and strain improvement: Present and outlook. Biotechnol Adv 2020; 53:107677. [PMID: 33290822 DOI: 10.1016/j.biotechadv.2020.107677] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/03/2020] [Accepted: 11/28/2020] [Indexed: 12/12/2022]
Abstract
Almost 40 years ago the first transgenic plant was generated through Agrobacterium tumefaciens-mediated transformation, which, until now, remains the method of choice for gene delivery into plants. Ever since, optimized Agrobacterium strains have been developed with additional (genetic) modifications that were mostly aimed at enhancing the transformation efficiency, although an optimized strain also exists that reduces unwanted plasmid recombination. As a result, a collection of very useful strains has been created to transform a wide variety of plant species, but has also led to a confusing Agrobacterium strain nomenclature. The latter is often misleading for choosing the best-suited strain for one's transformation purposes. To overcome this issue, we provide a complete overview of the strain classification. We also indicate different strain modifications and their purposes, as well as the obtained results with regard to the transformation process sensu largo. Furthermore, we propose additional improvements of the Agrobacterium-mediated transformation process and consider several worthwhile modifications, for instance, by circumventing a defense response in planta. In this regard, we will discuss pattern-triggered immunity, pathogen-associated molecular pattern detection, hormone homeostasis and signaling, and reactive oxygen species in relationship to Agrobacterium transformation. We will also explore alterations that increase agrobacterial transformation efficiency, reduce plasmid recombination, and improve biocontainment. Finally, we recommend the use of a modular system to best utilize the available knowledge for successful plant transformation.
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Affiliation(s)
- Jonas De Saeger
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jihae Park
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Marine Sciences, Incheon National University, Incheon 406-840, South Korea
| | - Hoo Sun Chung
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Stephen Depuydt
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.
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36
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Panicucci G, Iacopino S, De Meo E, Perata P, Weits DA. An Improved HRPE-Based Transcriptional Output Reporter to Detect Hypoxia and Anoxia in Plant Tissue. BIOSENSORS-BASEL 2020; 10:bios10120197. [PMID: 33287141 PMCID: PMC7761731 DOI: 10.3390/bios10120197] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/22/2023]
Abstract
Oxygen levels in plant tissues may vary, depending on metabolism, diffusion barriers, and environmental availability. Current techniques to assess the oxic status of plant cells rely primarily on invasive microoptodes or Clark-type electrodes, which are not optimally suited for experiments that require high spatial and temporal resolution. In this case, a genetically encoded oxygen biosensor is required instead. This article reports the design, test, and optimization of a hypoxia-signaling reporter, based on five-time repeated hypoxia-responsive promoter elements (HRPE) driving the expression of different reporter proteins. Specifically, this study aimed to improve its performance as a reporter of hypoxic conditions by testing the effect of different untranslated regions (UTRs) at the 5′ end of the reporter coding sequence. Next, we characterized an optimized version of the HRPE promoter (HRPE-Ω) in terms of hypoxia sensitivity and time responsiveness. We also observed that severe oxygen deficiency counteracted the reporter activity due to inhibition of GFP maturation, which requires molecular oxygen. To overcome this limitation, we therefore employed an oxygen-independent UnaG fluorescent protein-coupled to an O2-dependent mCherry fluorophore under the control of the optimized HRPE-Ω promoter. Remarkably, this sensor, provided a different mCherry/UnaG ratiometric output depending on the externally imposed oxygen concentration, providing a solution to distinguish between different degrees of tissue hypoxia. Moreover, a ubiquitously expressed UnaG-mCherry fusion could be used to image oxygen concentrations directly, albeit at a narrow range. The luminescent and fluorescent hypoxia-reporters described here can readily be used to conduct studies that involve anaerobiosis in plants.
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Affiliation(s)
- Gabriele Panicucci
- Biology Department, University of Pisa, 56126 Pisa, Italy; (G.P.); (S.I.)
| | - Sergio Iacopino
- Biology Department, University of Pisa, 56126 Pisa, Italy; (G.P.); (S.I.)
- Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy;
| | - Elisa De Meo
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
| | | | - Daan A. Weits
- Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy;
- Correspondence: ; Tel.: +39-050-881913
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Miguel VN, Ribichich KF, Giacomelli JI, Chan RL. Key role of the motor protein Kinesin 13B in the activity of homeodomain-leucine zipper I transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6282-6296. [PMID: 32882705 DOI: 10.1093/jxb/eraa379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
The sunflower (Helianthus annuus) homeodomain-leucine zipper I transcription factor HaHB11 conferred differential phenotypic features when it was expressed in Arabidopsis, alfalfa, and maize plants. Such differences were increased biomass, seed yield, and tolerance to flooding. To elucidate the molecular mechanisms leading to such traits and identify HaHB11-interacting proteins, a yeast two-hybrid screening of an Arabidopsis cDNA library was carried out using HaHB11 as bait. The sole protein identified with high confidence as interacting with HaHB11 was Kinesin 13B. The interaction was confirmed by bimolecular fluorescence complementation and by yeast two-hybrid assay. Kinesin 13B also interacted with AtHB7, the Arabidopsis closest ortholog of HaHB11. Histochemical analyses revealed an overlap between the expression patterns of the three genes in hypocotyls, apical meristems, young leaves, vascular tissue, axillary buds, cauline leaves, and cauline leaf nodes at different developmental stages. AtKinesin 13B mutants did not exhibit a differential phenotype when compared with controls; however, both HaHB11 and AtHB7 overexpressor plants lost, partially or totally, their differential phenotypic characteristics when crossed with such mutants. Altogether, the results indicated that Kinesin 13B is essential for the homeodomain-leucine zipper transcription factors I to exert their functions, probably via regulation of the intracellular distribution of these transcription factors by the motor protein.
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Affiliation(s)
- Virginia Natali Miguel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Karina Fabiana Ribichich
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Jorge Ignacio Giacomelli
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Raquel Lia Chan
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
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Suda H, Mano H, Toyota M, Fukushima K, Mimura T, Tsutsui I, Hedrich R, Tamada Y, Hasebe M. Calcium dynamics during trap closure visualized in transgenic Venus flytrap. NATURE PLANTS 2020; 6:1219-1224. [PMID: 33020606 DOI: 10.1038/s41477-020-00773-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 08/24/2020] [Indexed: 05/02/2023]
Abstract
The leaves of the carnivorous plant Venus flytrap, Dionaea muscipula (Dionaea) close rapidly to capture insect prey. The closure response usually requires two successive mechanical stimuli to sensory hairs on the leaf blade within approximately 30 s (refs. 1-4). An unknown biological system in Dionaea is thought to memorize the first stimulus and transduce the signal from the sensory hair to the leaf blade2. Here, we link signal memory to calcium dynamics using transgenic Dionaea expressing a Ca2+ sensor. Stimulation of a sensory hair caused an increase in cytosolic Ca2+ concentration ([Ca2+]cyt) starting in the sensory hair and spreading to the leaf blade. A second stimulus increased [Ca2+]cyt to an even higher level, meeting a threshold that is correlated to the leaf blade closure. Because [Ca2+]cyt gradually decreased after the first stimulus, the [Ca2+]cyt increase induced by the second stimulus was insufficient to meet the putative threshold for movement after about 30 s. The Ca2+ wave triggered by mechanical stimulation moved an order of magnitude faster than that induced by wounding in petioles of Arabidopsis thaliana5 and Dionaea. The capacity for rapid movement has evolved repeatedly in flowering plants. This study opens a path to investigate the role of Ca2+ in plant movement mechanisms and their evolution.
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Affiliation(s)
- Hiraku Suda
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Hiroaki Mano
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
- JST, PRESTO, Saitama, Japan
| | - Masatsugu Toyota
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
- Department of Botany, University of Wisconsin, Madison, WI, USA
| | - Kenji Fukushima
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Izuo Tsutsui
- Graduate School of Business Administration, Hitotsubashi University, Kunitachi, Japan
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Yosuke Tamada
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
- School of Engineering, Utsunomiya University, Utsunomiya, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan.
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.
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Hou W, Singh RK, Zhao P, Martins V, Aguilar E, Canto T, Tenllado F, Franklin G, Dias ACP. Overexpression of polygalacturonase-inhibiting protein (PGIP) gene from Hypericum perforatum alters expression of multiple defense-related genes and modulates recalcitrance to Agrobacterium tumefaciens in tobacco. JOURNAL OF PLANT PHYSIOLOGY 2020; 253:153268. [PMID: 32947246 DOI: 10.1016/j.jplph.2020.153268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 05/07/2023]
Abstract
Hypericum perforatum L is a remarkable source of high-value secondary metabolites with increasing applications in pharmaceutical industry. However, improvement in the production of secondary metabolites through genetic engineering is a demanding task, as H. perforatum is not amenable to Agrobacterium tumefaciens-mediated transformation. In this study, we identified a Polygalacturonase-inhibiting protein (PGIP) gene from a subtractive cDNA library of A. tumefaciens-treated H. perforatum suspension cells. The role of HpPGIP in defense against A. tumefaciens was analyzed in transgenic Nicotiana tabacum overexpressing HpPGIP alone or fused at the N-terminus to Phenolic oxidative coupling protein (Hyp-1), a gene that positively modulates resistance to A. tumefaciens. Furthermore, virus-induced gene silencing was employed to knock down the expression of the PGIP homologous in N. benthamiana. Results showed that Agrobacterium-mediated expression efficiency greatly decreased in both HpPGIP and Hyp-1-PGIP transgenic plants, as assessed by GUS staining assays. However, silencing of PGIP in N. benthamiana increased the resistance to A. tumefaciens rather than susceptibility, which correlated with induction of pathogenesis-related proteins (PRs). The expression of core genes involved in several defense pathways was also analyzed in transgenic tobacco plants. Overexpression of HpPGIP led to up-regulation of key genes involved in hormone signaling, microRNA-based gene silencing, homeostasis of reactive oxygen species, and the phenylpropanoid pathway. Overexpression of Hyp-1-PGIP seemed to enhance the effect of PGIP on the expression of most genes analyzed. Moreover, HpPGIP was detected in the cytoplasm, nucleus and the plasma membrane or cell wall by confocal microscopy. Overall, our findings suggest HpPGIP modulates recalcitrance to A. tumefaciens-mediated transformation in H. perforatum.
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Affiliation(s)
- Weina Hou
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Department of Biology, University of Minho, 4710-057, Braga, Portugal
| | - Rupesh Kumar Singh
- Centre of chemistry of Vila Real (CQ-VR), UTAD, 5000-801, Vila Real, Portugal
| | - Pan Zhao
- National Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Viviana Martins
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal
| | - Emmanuel Aguilar
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, 28040, Spain
| | - Tomás Canto
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, 28040, Spain
| | - Francisco Tenllado
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, 28040, Spain.
| | - Gregory Franklin
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Department of Biology, University of Minho, 4710-057, Braga, Portugal
| | - Alberto Carlos Pires Dias
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Department of Biology, University of Minho, 4710-057, Braga, Portugal; Center of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal.
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Lim GH, Kim SW, Ryu J, Kang SY, Kim JB, Kim SH. Upregulation of the MYB2 Transcription Factor Is Associated with Increased Accumulation of Anthocyanin in the Leaves of Dendrobium bigibbum. Int J Mol Sci 2020; 21:ijms21165653. [PMID: 32781758 PMCID: PMC7460623 DOI: 10.3390/ijms21165653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
Orchids with colorful leaves and flowers have significant ornamental value. Here, we used γ-irradiation-based mutagenesis to produce a Dendrobium bigibbum mutant that developed purple instead of the normal green leaves. RNA sequencing of the mutant plant identified 2513 differentially expressed genes, including 1870 up- and 706 downregulated genes. The purple leaf color of mutant leaves was associated with increased expression of genes that encoded key biosynthetic enzymes in the anthocyanin biosynthetic pathway. In addition, the mutant leaves also showed increased expression of several families of transcription factors including the MYB2 gene. Transient overexpression of D. biggibumMYB2 in Nicotiana benthamiana was associated with increased expression of endogenous anthocyanin biosynthesis genes. Interestingly, transient overexpression of orthologous MYB2 genes from other orchids did not upregulate expression of endogenous anthocyanin biosynthesis genes. Together, these results suggest that the purple coloration of D. biggibum leaves is at least associated with increased expression of the MYB2 gene, and the MYB2 orthologs from orchids likely function differently, regardless of their high level of similarity.
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Affiliation(s)
- Gah-Hyun Lim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Korea; (G.-H.L.); (S.W.K.); (J.R.); (S.-Y.K.); (J.-B.K.)
| | - Se Won Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Korea; (G.-H.L.); (S.W.K.); (J.R.); (S.-Y.K.); (J.-B.K.)
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Korea; (G.-H.L.); (S.W.K.); (J.R.); (S.-Y.K.); (J.-B.K.)
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Korea; (G.-H.L.); (S.W.K.); (J.R.); (S.-Y.K.); (J.-B.K.)
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Korea; (G.-H.L.); (S.W.K.); (J.R.); (S.-Y.K.); (J.-B.K.)
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Korea; (G.-H.L.); (S.W.K.); (J.R.); (S.-Y.K.); (J.-B.K.)
- Correspondence: ; Tel.: +82-63-570-3318; Fax: +82-63-570-3811
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Khezri G, Baghban Kohneh Rouz B, Ofoghi H, Davarpanah SJ. Heterologous expression of biologically active Mambalgin-1 peptide as a new potential anticancer, using a PVX-based viral vector in Nicotiana benthamiana. PLANT CELL, TISSUE AND ORGAN CULTURE 2020; 142:241-251. [PMID: 32836586 PMCID: PMC7323601 DOI: 10.1007/s11240-020-01838-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Mambalgin-1 is a peptide that acts as a potent analgesic through inhibiting acid-sensing ion channels (ASIC) in nerve cells. Research has shown that ASIC channels are involved in the proliferation and growth of cancer cells; therefore, Mambalgin-1 can be a potential anti-cancer by inhibiting these channels. In the present study, the Nicotiana benthamiana codon optimized Mambalgin-1 gene was synthesized and cloned in PVX (potato virus X) viral vector. The two cultures of Agrobacterium containing Mambalgin-1 and P19 silencing suppressor genes were co-agroinfiltrated into N. benthamiana leaves. Five days post infiltration, the production of recombinant Mambalgin-1 was determined by western blotting. For biological activity, MTT (3(4, 5-dimethylthiazole-2-yl)-2, 5-diphenyltetrazolium bromide) was analyzed for the cytotoxicity recombinant Mambalgin-1 from the transformed plants on nervous (SH-SY5Y) and breast (MCF7) cancer cells. The results showed that the plants expressing open reading frame of Mambalgin-1 showed recombinant 7.4 kDa proteins in the entire plant extract. In the MTT test, it was found that Mambalgin-1 had cytotoxic effects on SH-SY5Y cancer cells, yet no effects on MCF7 cancer cells were observed. According to the results, the expression of the biologically active recombinant Mambalgin-1 in the transformed plant leaves was confirmed and Mambalgin-1 can also have anti-cancer (inhibition of ASIC channels) potential along with its already known analgesic effect.
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Affiliation(s)
- Ghaffar Khezri
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran
| | | | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Seyed Javad Davarpanah
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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García-Ulloa A, Sanjurjo L, Cimini S, Encina A, Martínez-Rubio R, Bouza R, Barral L, Estévez-Pérez G, Novo-Uzal E, De Gara L, Pomar F. Overexpression of ZePrx in Nicotiana tabacum Affects Lignin Biosynthesis Without Altering Redox Homeostasis. FRONTIERS IN PLANT SCIENCE 2020; 11:900. [PMID: 32676088 PMCID: PMC7333733 DOI: 10.3389/fpls.2020.00900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/02/2020] [Indexed: 05/30/2023]
Abstract
Class III plant peroxidases (Prxs) are involved in the oxidative polymerization of lignins. Zinnia elegans Jacq. Basic peroxidase (ZePrx) has been previously characterized as capable of catalyzing this reaction in vitro and the role in lignin biosynthesis of several of its Arabidopsis thaliana homologous has been previously confirmed. In the present work, ZePrx was overexpressed in Nicotiana tabacum to further characterize its function in planta with particular attention to its involvement in lignin biosynthesis. Since Prxs are known to alter ROS levels by using them as electron acceptor or producing them in their catalytic activity, the impact of this overexpression in redox homeostasis was studied by analyzing the metabolites and enzymes of the ascorbate-glutathione cycle. In relation to the modification induced by ZePrx overexpression in lignin composition and cellular metabolism, the carbohydrate composition of the cell wall as well as overall gene expression through RNA-Seq were analyzed. The obtained results indicate that the overexpression of ZePrx caused an increase in syringyl lignin in cell wall stems, suggesting that ZePrx is relevant for the oxidation of sinapyl alcohol during lignin biosynthesis, coherently with its S-peroxidase nature. The increase in the glucose content of the cell wall and the reduction of the expression of several genes involved in secondary cell wall biosynthesis suggests the occurrence of a possible compensatory response to maintain cell wall properties. The perturbation of cellular redox homeostasis occurring as a consequence of ZePrx overexpression was kept under control by an increase in APX activity and a reduction in ascorbate redox state. In conclusion, our results confirm the role of ZePrx in lignin biosynthesis and highlight that its activity alters cellular pathways putatively aimed at maintaining redox homeostasis.
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Affiliation(s)
- Alba García-Ulloa
- Departamento de Biología, Centro de Investigaciones Científicas Avanzadas, Universidade da Coruña, A Coruña, Spain
| | - Laura Sanjurjo
- Departamento de Biología, Centro de Investigaciones Científicas Avanzadas, Universidade da Coruña, A Coruña, Spain
| | - Sara Cimini
- Unit of Food Science and Human Nutrition, Department of Science and Technology for Humans and the Environment, Campus Bio-Medico University, Rome, Italy
| | - Antonio Encina
- Área de Fisiología Vegetal, Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, León, Spain
| | - Romina Martínez-Rubio
- Área de Fisiología Vegetal, Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, León, Spain
| | - Rebeca Bouza
- Grupo de Polímeros, Departamento de Física y Ciencias de la Tierra Escuela Universitaria Politécnica, Universidade da Coruña, Serantes, Ferrol, Spain
| | - Luis Barral
- Grupo de Polímeros, Departamento de Física y Ciencias de la Tierra Escuela Universitaria Politécnica, Universidade da Coruña, Serantes, Ferrol, Spain
| | | | | | - Laura De Gara
- Unit of Food Science and Human Nutrition, Department of Science and Technology for Humans and the Environment, Campus Bio-Medico University, Rome, Italy
| | - Federico Pomar
- Departamento de Biología, Centro de Investigaciones Científicas Avanzadas, Universidade da Coruña, A Coruña, Spain
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Tian Y, Du J, Wu H, Guan X, Chen W, Hu Y, Fang L, Ding L, Li M, Yang D, Yang Q, Zhang T. The transcription factor MML4_D12 regulates fiber development through interplay with the WD40-repeat protein WDR in cotton. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3499-3511. [PMID: 32149350 PMCID: PMC7475258 DOI: 10.1093/jxb/eraa104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 02/28/2020] [Indexed: 05/24/2023]
Abstract
In planta, a vital regulatory complex, MYB-basic helix-loop-helix (bHLH)-WD40 (MBW), is involved in trichome development and synthesis of anthocyanin and proanthocyanin in Arabidopsis. Usually, WD40 proteins provide a scaffold for protein-protein interaction between MYB and bHLH proteins. Members of subgroup 9 of the R2R3 MYB transcription factors, which includes MYBMIXTA-Like (MML) genes important for plant cell differentiation, are unable to interact with bHLH. In this study, we report that a cotton (Gossypium hirsutum) seed trichome or lint fiber-related GhMML factor, GhMML4_D12, interacts with a diverged WD40 protein (GhWDR) in a process similar to but different from that of the MBW ternary complex involved in Arabidopsis trichome development. Amino acids 250-267 of GhMML4_D12 and the first and third WD40 repeat domains of GhWDR determine their interaction. GhWDR could rescue Arabidopsis ttg1 to its wild type, confirming its orthologous function in trichome development. Our findings shed more light towards understanding the key role of the MML and WD40 families in plants and in the improvement of cotton fiber production.
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Affiliation(s)
- Yue Tian
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Jingjing Du
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Huaitong Wu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xueying Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Weihang Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yan Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Lei Fang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Linyun Ding
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Menglin Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Duofeng Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Qinli Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
| | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, P. R. China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
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44
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Abd-Aziz N, Tan BC, Rejab NA, Othman RY, Khalid N. A New Plant Expression System for Producing Pharmaceutical Proteins. Mol Biotechnol 2020; 62:240-251. [PMID: 32108286 DOI: 10.1007/s12033-020-00242-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In the past decade, interest in the production of recombinant pharmaceutical proteins in plants has tremendously progressed because plants do not harbor mammalian viruses, are economically competitive, easily scalable, and capable of carrying out complex post-translational modifications required for recombinant pharmaceutical proteins. Mucuna bracteata is an essential perennial cover crop species widely planted as an underground cover in oil palm and rubber plantations. As a legume, they have high biomass, thrive in its habitat, and can fix nitrogen. Thus, M. bracteata is a cost-efficient crop that shows ideal characteristics as a platform for mass production of recombinant protein. In this study, we established a new platform for the transient production of a recombinant protein in M. bracteata via vacuum-assisted agro-infiltration. Five-week-old M. bracteata plants were vacuum infiltrated with Agrobacterium tumefaciens harboring a plasmid that encodes for an anti-toxoplasma immunoglobulin (IgG) under different parameters, including trifoliate leaf positional effects, days to harvest post-infiltration, and the Agrobacterium strain used. Our results showed that vacuum infiltration of M. bracteata plant with A. tumefaciens strain GV3101 produced the highest concentration of heterologous protein in its bottom trifoliate leaf at 2 days post-infiltration. The purified anti-toxoplasma IgG was then analyzed using Western blot and ELISA. It was demonstrated that, while structural heterogeneity existed in the purified anti-toxoplasma IgG from M. bracteata, its transient expression level was two-fold higher than the model platform, Nicotiana benthamiana. This study has laid the foundation towards establishing M. bracteata as a potential platform for the production of recombinant pharmaceutical protein.
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Affiliation(s)
- Nazrin Abd-Aziz
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nur Ardiyana Rejab
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Rofina Yasmin Othman
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Norzulaani Khalid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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45
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Thompson MG, Moore WM, Hummel NFC, Pearson AN, Barnum CR, Scheller HV, Shih PM. Agrobacterium tumefaciens: A Bacterium Primed for Synthetic Biology. BIODESIGN RESEARCH 2020; 2020:8189219. [PMID: 37849895 PMCID: PMC10530663 DOI: 10.34133/2020/8189219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 04/26/2020] [Indexed: 10/19/2023] Open
Abstract
Agrobacterium tumefaciens is an important tool in plant biotechnology due to its natural ability to transfer DNA into the genomes of host plants. Genetic manipulations of A. tumefaciens have yielded considerable advances in increasing transformational efficiency in a number of plant species and cultivars. Moreover, there is overwhelming evidence that modulating the expression of various mediators of A. tumefaciens virulence can lead to more successful plant transformation; thus, the application of synthetic biology to enable targeted engineering of the bacterium may enable new opportunities for advancing plant biotechnology. In this review, we highlight engineering targets in both A. tumefaciens and plant hosts that could be exploited more effectively through precision genetic control to generate high-quality transformation events in a wider range of host plants. We then further discuss the current state of A. tumefaciens and plant engineering with regard to plant transformation and describe how future work may incorporate a rigorous synthetic biology approach to tailor strains of A. tumefaciens used in plant transformation.
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Affiliation(s)
- Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
| | - William M. Moore
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Niklas F. C. Hummel
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
| | - Allison N. Pearson
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Collin R. Barnum
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
| | - Henrik V. Scheller
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Patrick M. Shih
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
- Genome Center, University of California-Davis, Davis, CA, USA
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46
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Ogura T, Goeschl C, Filiault D, Mirea M, Slovak R, Wolhrab B, Satbhai SB, Busch W. Root System Depth in Arabidopsis Is Shaped by EXOCYST70A3 via the Dynamic Modulation of Auxin Transport. Cell 2020; 178:400-412.e16. [PMID: 31299202 DOI: 10.1016/j.cell.2019.06.021] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/12/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022]
Abstract
Root system architecture (RSA), the distribution of roots in soil, plays a major role in plant survival. RSA is shaped by multiple developmental processes that are largely governed by the phytohormone auxin, suggesting that auxin regulates responses of roots that are important for local adaptation. However, auxin has a central role in numerous processes, and it is unclear which molecular mechanisms contribute to the variation in RSA for environmental adaptation. Using natural variation in Arabidopsis, we identify EXOCYST70A3 as a modulator of the auxin system that causes variation in RSA by acting on PIN4 protein distribution. Allelic variation and genetic perturbation of EXOCYST70A3 lead to alteration of root gravitropic responses, resulting in a different RSA depth profile and drought resistance. Overall our findings suggest that the local modulation of the pleiotropic auxin pathway can gives rise to distinct RSAs that can be adaptive in specific environments.
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Affiliation(s)
- Takehiko Ogura
- Plant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Christian Goeschl
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Daniele Filiault
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Madalina Mirea
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Radka Slovak
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Bonnie Wolhrab
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Santosh B Satbhai
- Plant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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47
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Zhang Y, Zhang Q, Chen QJ. Agrobacterium-mediated delivery of CRISPR/Cas reagents for genome editing in plants enters an era of ternary vector systems. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1491-1498. [PMID: 32279281 DOI: 10.1007/s11427-020-1685-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/19/2020] [Indexed: 12/24/2022]
Abstract
Lack of appropriate methods for delivery of genome-editing reagents is a major barrier to CRISPR/Cas-mediated genome editing in plants. Agrobacterium-mediated genetic transformation (AMGT) is the preferred method of CRISPR/Cas reagent delivery, and researchers have recently made great improvements to this process. In this article, we review the development of AMGT and AMGT-based delivery of CRISPR/Cas reagents. We give an overview of the development of AMGT vectors including binary vector, superbinary vector, dual binary vector, and ternary vector systems. We also review the progress in Agrobacterium genomics and Agrobacterium genetic engineering for optimal strains. We focus in particular on the ternary vector system and the resources we developed. In summary, it is our opinion that Agrobacterium-mediated CRISPR/Cas genome editing in plants is entering an era of ternary vector systems, which are often integrated with morphogenic regulators. The new vectors described in this article are available from Addgene and/or MolecularCloud for sharing with academic investigators for noncommercial research.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qiang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qi-Jun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. .,Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
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48
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Liu S, Ma J, Liu H, Guo Y, Li W, Niu S. An efficient system for Agrobacterium-mediated transient transformation in Pinus tabuliformis. PLANT METHODS 2020; 16:52. [PMID: 32308730 PMCID: PMC7149934 DOI: 10.1186/s13007-020-00594-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/03/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Functional genomic studies using genetics approaches of conifers are hampered by the complex and enormous genome, long vegetative growth period, and exertion in genetic transformation. Thus, the research carried out on gene function in Pinus tabuliformis is typically performed by heterologous expression based on the model plant Arabidopsis. However, due to the evolutionary and vast diversification from non-flowering (gymnosperms) to flowering (angiosperms) plants, several key differences may alter the underlying genetic concerns and the analysis of variants. Therefore, it is essential to develop an efficient genetic transformation and gene function identification protocol for P. tabuliformis. RESULTS In the present study we established a highly efficient transgene Agrobacterium-mediated transient expression system for P. tabuliformis. Using a β-glucuronidase gene (GUS) as a reporter gene expression, the highest transformation efficiency (70.1%) was obtained by co-cultivation with Agrobacterium strain GV3101 at an optical density at 600 nm of 0.8, with 150 μM acetosyringone for 30 min followed by 3 days in the dark at 23 ± 1 °C. This protocol would be applied to other conifers; GUS staining was observed 24 h post-infection. CONCLUSIONS We report a simple, fast, and resilient system for transient Agrobacterium-mediated transformation high-level expression of target genes in P. tabuliformis, which will also improve transformation efficiency in other conifer species.
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Affiliation(s)
- Shuangwei Liu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Jingjing Ma
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Hongmei Liu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Yingtian Guo
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Shihui Niu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
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49
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Gramzow L, Lobbes D, Innard N, Theißen G. Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense-transcribed sequences. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:401-419. [PMID: 31571291 DOI: 10.1111/tpj.14550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Some microRNAs (miRNAs) are key regulators of developmental processes, mainly by controlling the accumulation of transcripts encoding transcription factors that are important for morphogenesis. MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants. Here we study the convergent evolution of two MIRNA (MIR) gene families, named MIR444 and MIR824, targeting members of the same clade of MIKCC -group MADS-box genes. We show that these two MIR genes most likely originated independently in monocots (MIR444) and in Brassicales (eudicots, MIR824). We provide evidence that, in both cases, the future target gene was transcribed in antisense prior to the evolution of the MIR genes. Both MIR genes then likely originated by a partial inverted duplication of their target genes, resulting in natural antisense organization of the newly evolved MIR gene and its target gene at birth. We thus propose a model for the origin of MIR genes, MEPIDAS (MicroRNA Evolution by Partial Inverted Duplication of Antisense-transcribed Sequences). MEPIDAS is a refinement of the inverted duplication hypothesis. According to MEPIDAS, a MIR gene evolves at a genomic locus at which the future target gene is also transcribed in the antisense direction. A partial inverted duplication at this locus causes the antisense transcript to fold into a stem-loop structure that is recognized by the miRNA biogenesis machinery to produce a miRNA that regulates the gene at this locus. Our analyses exemplify how to elucidate the origin of conserved miRNAs by comparative genomics and will guide future studies. OPEN RESEARCH BADGE: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/genbank/.
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Affiliation(s)
- Lydia Gramzow
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Dajana Lobbes
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Nathan Innard
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
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Tuo D, Zhou P, Zhao G, Yan P, Tan D, Li X, Shen W. A Double Mutation in the Conserved Motifs of the Helper Component Protease of Papaya Leaf Distortion Mosaic Virus for the Generation of a Cross-Protective Attenuated Strain. PHYTOPATHOLOGY 2020; 110:187-193. [PMID: 31516080 DOI: 10.1094/phyto-09-19-0328-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Potyviral helper component protease (HC-Pro), as a major determinant of symptom expression in susceptible plants, is a likely target candidate in the production of attenuated strains for cross-protection. In this study, single or double mutations of Lys (K) to Glu (E) in the Lys-Ile-Thr-Cys motif and Arg (R) to Ile (I) in the Phe-Arg-Asn-Lys motif of the HC-Pro from the severe papaya leaf distortion mosaic virus strain DF (PLDMV-DF) reduced symptom expression and virus accumulation in infected papaya (Carica papaya) plants. The papaya plants infected with the attenuated double mutant of PLDMV-EI presented as symptomless. PLDMV-EI provided effective protection against PLDMV-DF infection in three papaya cultivars and had no effect on plant growth and development. Our result showed that PLDMV-EI is a promising mild strain for the practical use of cross-protection in the field.
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Affiliation(s)
- Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
| | - Guangyuan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
| | - Dong Tan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
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